Despite protests by animal-rights activists and some farmers, the Department of Agriculture is going ahead with a requirement that dairy cows sold in a new herd-buyout program be branded on their faces with hot irons.

"They believe it's inhumane. We don't," said department official Thomas VonGarlem after a meeting yesterday with a group from the Humane Society of the United States. "We've agreed we'll think about it over the weekend, if we will change or hold tight."

But the society's Dr. Michael Fox, urging the department to use other methods of identifying cows and calves that go into the program, said he was not optimistic. "The bureaucrats have a Procrustean mentality; the veterinarians are insensitive to the issue," he said.

The department's rules require that full-sized dairy cows be marked with a three-inch "X" on the jaw. Smaller calves entered in the program must carry two-inch face brands.

Fox said that he and other animal-welfare advocates fear that the branding requirements, carried out by inexperienced farmers, could lead to serious damage and mutilation of the cows that the government will buy in the program.

Fox said that department officials rejected suggestions that the cows be marked with indelible dye tattoos in the ears or nose instead of hot brands.

"What is needed long-term is an identification system that treats both the farmers and the animals more humanely. We would hope that the USDA would begin now to develop less barbaric methods. The technology exists; all we need is a commitment to use it."

The department's branding rules, issued to farmers as part of the herd-buyout program, acknowledged the possibility of damage to animals.

"It may be necessary to experiment a bit to find the right heat," the notice said. "If too hot, the iron will start a hair fire . . . . Burning deeper than necessary to obtain the brand impression will result in blotched sores that take too long to heal."

VonGarlem conceded that some farmers have found the branding requirements "very objectionable." But he added that the hot-iron approach was needed as protection against cheating by farmers who might "switch" animals after they have sold herds to the government.

"The taxpayers cannot afford the luxury of paying for an expensive 3,000-pound animal and having a farmer give us a cull cow instead," he said.

The whole herd-buyout program, which will get under way next month, is part of the 1985 farm bill. Its aim is to reduce dairy surpluses, and their high cost to the government, by paying farmers to give up dairying.

Cows purchased by the government will be taken out of production and sent to slaughter. To protect the cattle industry from a market glut and lower prices, the farm law also requires the Agriculture Department to buy $200 million worth of beef for federal feeding programs each year.

VonGarlem said the department decided on face markings, rather than flank markings, for cows purchased in the program because branding rights on other parts of the animals are regulated by states and counties.

"The jaw is a reserved area for USDA programs," he said.

Fox, however, was unforgiving. "It's all economics," he said. "The USDA has been caught with its pants down on this. There are other ways to identify the cows without being injurious."